Hey I finally figured this out, leaving it here in case anyone else is having the same issue
Delete the 'persistent' file in the AppData\Roaming\RenPy folder then go back to the Seven Kingdom Princess Problem \game\saves folder and delete the 'persistent' file there
Simply deleting the folder in AppData\Roaming\RenPy will cause the game to pick up on the 'persistent' file in the SKPP \game\saves folder. This will then sync the file there back into the AppData\Roaming\RenPy folder.
To put it simply, both the universal persistent file and the local persistent file must be deleted to get a clean slate. If you only delete one but not the other, then the game will continue to check both locations and sync to the one that has the most progress.